Introduction: Lethal congenital anomalies (LCA) are anomalies associated with early stillbirth or newborn death. Currently, there are no data on the incidence of LCAs in Peru. Objectives: To estimate the cumulative incidence of LCAs in Peru, the Department of Lima, and six hospitals located in the city of Lima (Peru), and to describe the characteristics of LCA cases reported between 2012 and 2016 at Instituto Nacional Materno Perinatal (INMP), located in Lima, Perú. Materials and methods: Cumulative incidence of LCAs in Peru was determined based on the cases reported in a five-year period, which varied depending on data accessibility (20112015 and 2012-2016). In addition, the medical records of neonates with LCA registered at INMP were reviewed to identify the characteristics of these cases. Results: Cumulative incidence of LCAs in Peru was 0.89 cases per 10 000 newborns, while at INMP it was 7.19 cases. Out of 48 newborns with LCAs treated at INMP during the study period, 54.2% were born with neonatal depression, and 83.3% died during their hospital stay. Conclusion: Cumulative incidences of LCAs reported here (Lima, Department of Lima, and Peru) were lower than those described by international epidemiological surveillance systems, which might be caused due to shortcomings related to the registration of these cases in the health institutions and records analyzed here.